Sorry, ignore what I said for the aside: you take the average of 10 volumes starting at volume 11. Better than taking the first 10. Sorry for my Sunday early morning confusion :-)
But the main issue remains, that mc flirt_acc does not correct for motion as well as mcflirt. Let me know your thoughts on why this may be. Thanks, - Julien > On Dec 14, 2014, at 10:14 AM, Julien Dubois <[email protected]> wrote: > > Dear all, > > I want to weigh in here: the current default behavior of the pipeline is not > doing a good job at motion correction (in my own data). > > First a quick digression: > The code in global/mcflirt_acc.sh indicates that you are taking the 10th > volume as a reference, in the absence of a supplied reference: > line 29: > ${FSLDIR}/bin/fslroi $input ${output}_ref 10 10 > I think that maybe you meant to take the average of the first 10 volumes (as > Greg B. indicated, and given the following lines of code); so line 29 should > likely be changed into: > ${FSLDIR}/bin/fslroi $input ${output}_ref 0 10 > > But I don't think this is where the issue comes from. Indeed, running mcflirt > with the 10th volume gives a fine result. There is thus something else in > mcflirt_acc that is not functioning properly (at least for data other than > HCP), compared to the standard FSL's mcflirt. > > Can you give the rationale for writing your own mcflirt function > (mcflirt_acc.sh), and explain how it differs from FSL's mcflirt? (I could > also go compare with the source code for mcflirt, but I thought I would ask > directly since you probably had a good reason) > > Thanks! > - Julien > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
